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Sample GSM5176172

Query DataSets for GSM5176172

Status

Public on Sep 13, 2022

Title

WT Cu2

Sample type

SRA

Source name

Batch culture Mueller Hinton broth

Organism

Acinetobacter baumannii

Characteristics

strain: ATCC 17978
genotype: Wild-type
growth phase: Exponential
treatment: CuSO4

Extracted molecule

total RNA

Extraction protocol

Bacterial cells were collected, flash frozen on dry ice ethanol bath, and RNA was harvested using Trizol (Ambion) reagent. For isolation and purification of total RNA from cells, RNeasy Qiagen was used.
Libraries were constructed using Universal Prokaryotic RNA-Seq Library preparation kit (Tecan, USA) according to the manufacturer protocol.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Basecalling was done using bcl2fastq2 V2.20 (Illumina, USA).
QC was performed using fastQC (v0.11.9)
Reads were trimmed using bbduk (v38.79) using the adapters.fa file provided with bbduk and parameters ktrim=r k=23 mink=11 hdist=1 qtrim2=t trimq=10 tpe tbo
Reads were mapped using bbmap (v38.79) with parameters k=13 and ambig=toss against the Acinetobacter baumannii genome (accession CP000522) and plasmids (accessions CP000523, CP012004, CP012005)
Reads were sorted using samtools (v1.6)
Reads over CDS features were quantified using HTSeq (v0.12.4)
Genome_build: CP000522.1, CP000523.1, CP012004.1, CP012005.1
Supplementary_files_format_and_content: Tab separated values containing read counts per feature in each condition

Submission date

Mar 17, 2021

Last update date

Sep 13, 2022

Contact name

Lars Barquist

E-mail(s)

[email protected]

Organization name

Helmholtz Institute for RNA-based Infection Research

Street address

Josef-Schneider-Straße 2 / Bau D15